OSError: "Unable to open file (file signature not found)" h5py/_objects.pyx:55 related error

[suniliisc]

I am experiencing the following error while saving cluster/msm etc.

Going through the tutorial 04-msm-analysis at ( http://www.emma-project.org/latest/tutorials/notebooks/04-msm-analysis.html)

I have attached the output of conda list. (https://github.com/markovmodel/PyEMMA/files/10069918/conda_list.csv)

Executed command: cluster.save('nb4.pyemma', model_name='doublewell_cluster', overwrite=True)

The API at (http://www.emma-project.org/latest/tutorials/notebooks/04-msm-analysis.html) also has a similar error. I got the following error:

OSError Traceback (most recent call last) Input In [63], in <cell line: 1>() ----> 1 cluster.save('nb4.pyemma', model_name='doublewell_cluster', overwrite=True)

File ~/anaconda3/envs/MSM/lib/python3.8/site-packages/pyemma/_base/serialization/serialization.py:238, in SerializableMixIn.save(self, file_name, model_name, overwrite, save_streaming_chain) 212 def save(self, file_name, model_name='default', overwrite=False, save_streaming_chain=False): 213 r""" saves the current state of this object to given file and name. 214 215 Parameters (...) 236 >>> np.testing.assert_equal(m.P, inst_restored.P) # doctest: +SKIP 237 """ --> 238 from pyemma._base.serialization.h5file import H5File 239 try: 240 with H5File(file_name=file_name, mode='a') as f:

File ~/anaconda3/envs/MSM/lib/python3.8/site-packages/pyemma/_base/serialization/h5file.py:22, in 20 import numpy as np 21 from io import BytesIO ---> 22 from .pickle_extensions import HDF5PersistentPickler 24 author = 'marscher' 26 logger = logging.getLogger(name)

File ~/anaconda3/envs/MSM/lib/python3.8/site-packages/pyemma/_base/serialization/pickle_extensions.py:68, in 64 pass 67 # we cache this during runtime ---> 68 _DEFAULT_BLOSC_OPTIONS = _check_blosc_avail() 71 class HDF5PersistentPickler(Pickler): 72 # stores numpy arrays during pickling in given hdf5 group. 73 def init(self, group, file):

File ~/anaconda3/envs/MSM/lib/python3.8/site-packages/pyemma/_base/serialization/pickle_extensions.py:46, in _check_blosc_avail() 44 fid, name = tempfile.mkstemp() 45 try: ---> 46 with h5py.File(name) as h5f: 47 try: 48 h5f.create_dataset('test', shape=(1,1), **blosc_opts)

File ~/anaconda3/envs/MSM/lib/python3.8/site-packages/h5py/_hl/files.py:533, in File.init(self, name, mode, driver, libver, userblock_size, swmr, rdcc_nslots, rdcc_nbytes, rdcc_w0, track_order, fs_strategy, fs_persist, fs_threshold, fs_page_size, page_buf_size, min_meta_keep, min_raw_keep, locking, alignment_threshold, alignment_interval, kwds) 525 fapl = make_fapl(driver, libver, rdcc_nslots, rdcc_nbytes, rdcc_w0, 526 locking, page_buf_size, min_meta_keep, min_raw_keep, 527 alignment_threshold=alignment_threshold, 528 alignment_interval=alignment_interval, 529 kwds) 530 fcpl = make_fcpl(track_order=track_order, fs_strategy=fs_strategy, 531 fs_persist=fs_persist, fs_threshold=fs_threshold, 532 fs_page_size=fs_page_size) --> 533 fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr) 535 if isinstance(libver, tuple): 536 self._libver = libver

File ~/anaconda3/envs/MSM/lib/python3.8/site-packages/h5py/_hl/files.py:226, in make_fid(name, mode, userblock_size, fapl, fcpl, swmr) 224 if swmr and swmr_support: 225 flags |= h5f.ACC_SWMR_READ --> 226 fid = h5f.open(name, flags, fapl=fapl) 227 elif mode == 'r+': 228 fid = h5f.open(name, h5f.ACC_RDWR, fapl=fapl)

File h5py/_objects.pyx:54, in h5py._objects.with_phil.wrapper()

File h5py/_objects.pyx:55, in h5py._objects.with_phil.wrapper()

File h5py/h5f.pyx:106, in h5py.h5f.open()

OSError: Unable to open file (file signature not found)

---

• Pyemma 2.5.7 and python 3.8.13
• Ubuntu 18.04.6 LTS

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.